Structure of the DNA-EcoRI Endonuclease Recognition Complex

Abstract

The 3 Å structure of the co-crystalline recognition complex between EcoRI endonuclease and the cognate oligonucleotide TCGCGAATTCGCG has been solved by the ISIR method using a platinum isomorphous derivative [1,2,3]. Refinement is in progress. The endonuclease-DNA recognition complex consists of a distorted double helix and a protein dimer composed of identical subunits related by a two-fold axis of rotational symmetry (see Fig. 1). The distortions of the DNA are not seen in the crystal structure of the dodecamer, CGCGAATTCGCG [4]; hence they are induced by the binding of the protein. The distortions are concentrated into separate features which are localized disruptions of the double helical symmetry. These disruptions appear to have structural consequences which propagate over long distances through the DNA via twisting and perhaps bending effects. They are therefore referred to as neo-kinks (see Figs. 2 and 3). The type I neo-kink spans the central two-fold symmetry axis of the complex and it introduces a net unwinding of 25° into the DNA. This increases the separation of the DNA backbones across the major groove thereby facilitating access by the protein to the base edges, which are at the floor of the groove. The type-I neo-kink also re-aligns adjacent adenine residues within the central AATT tetranucleotide so as to create the detailed geometry necessary for amino acid side chains to bridge across these purines (see below).